As Unai Emery's men trailed 2-0 after their first-leg defeat at the Roazhon Park, the London club rose to the occasion when Pierre-Emerick Aubameyang opened the scoring in the fifth minute.
The French-born Gabon global was also involved in Arsenal's second 10 minutes later, although Rennes were right to feel aggrieved that the goal was allowed to stand.
Aubameyang kept Ramsey's pass in play, but the Gabonese striker looked to be stood in an offside position before picking out Maitland-Niles at the back post.
"It was very clearly an injustice, it was a manifest error", Stéphan said.
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"There was no need for the VAR to see the offside".
Aubameyang had not scored in the competition since September so breaking his duck to get Arsenal up and running was timely, then he struck again late on for his sixth brace of the season in all competitions.
Having saved the day for the Gunners, Aubameyang saw it fit to masquerade in a hero's outfit and went ahead to put on a mask of popular Marvel superhero Black Panther. "The next match is the most important for us", Emery said.
"I needed a mask that would represent me", Aubameyang told BT Sport. "Black Panther.in Africa and Gabon we are called the Black Panthers so it represents me - that's it".